scholarly journals Gene Function Rather than Reproductive Mode Drives the Evolution of RNA Helicases in Sexual and Apomictic Boechera

2020 ◽  
Vol 12 (5) ◽  
pp. 656-673 ◽  
Author(s):  
Markus Kiefer ◽  
Berit H Nauerth ◽  
Christopher Volkert ◽  
David Ibberson ◽  
Anna Loreth ◽  
...  
Keyword(s):  
Gene Function ◽  
Higher Plants ◽  
Reproductive Mode ◽  
Deleterious Mutations ◽  
Rna Helicases ◽  
Germline Development ◽  
Allelic Variants ◽  
High Sequence Conservation ◽  
C And N ◽  
Mutant Lines

Abstract In higher plants, sexual and asexual reproductions through seeds (apomixis) have evolved as alternative strategies. Evolutionary advantages leading to coexistence of both reproductive modes are currently not well understood. It is expected that accumulation of deleterious mutations leads to a rapid elimination of apomictic lineages from populations. In this line, apomixis originated repeatedly, likely from deregulation of the sexual pathway, leading to alterations in the development of reproductive lineages (germlines) in apomicts as compared with sexual plants. This potentially involves mutations in genes controlling reproduction. Increasing evidence suggests that RNA helicases are crucial regulators of germline development. To gain insights into the evolution of 58 members of this diverse gene family in sexual and apomictic plants, we applied target enrichment combined with next-generation sequencing to identify allelic variants from 24 accessions of the genus Boechera, comprising sexual, facultative, and obligate apomicts. Interestingly, allelic variants from apomicts did not show consistently increased mutation frequency. Either sequences were highly conserved in any accession, or allelic variants preferentially harbored mutations in evolutionary less conserved C- and N-terminal domains, or presented high mutation load independent of the reproductive mode. Only for a few genes allelic variants harboring deleterious mutations were only identified in apomicts. To test if high sequence conservation correlates with roles in fundamental cellular or developmental processes, we analyzed Arabidopsis thaliana mutant lines in VASA-LIKE (VASL), and identified pleiotropic defects during ovule and reproductive development. This indicates that also in apomicts mechanisms of selection are in place based on gene function.

scholarly journals Extracellular Localisation of the C-Terminus of DDX4 Confirmed by Immunocytochemistry and Fluorescence-Activated Cell Sorting

Cells ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 578 ◽  
Author(s):  
Yvonne L. Clarkson ◽  
Emma Weatherall ◽  
Martin Waterfall ◽  
Marie McLaughlin ◽  
Haojiang Lu ◽  
...  
Keyword(s):  
Cell Surface ◽  
Cell Sorting ◽  
Ovarian Tissue ◽  
Fluorescence Activated Cell Sorting ◽  
Rt Pcr ◽  
Rna Helicases ◽  
Dead Box ◽  
C Terminus ◽  
Expression Construct ◽  
C And N

Putative oogonial stem cells (OSCs) have been isolated by fluorescence-activated cell sorting (FACS) from adult human ovarian tissue using an antibody against DEAD-box helicase 4 (DDX4). DDX4 has been reported to be germ cell specific within the gonads and localised intracellularly. White et al. (2012) hypothesised that the C-terminus of DDX4 is localised on the surface of putative OSCs but is internalised during the process of oogenesis. This hypothesis is controversial since it is assumed that RNA helicases function intracellularly with no extracellular expression. To determine whether the C-terminus of DDX4 could be expressed on the cell surface, we generated a novel expression construct to express full-length DDX4 as a DsRed2 fusion protein with unique C- and N-terminal epitope tags. DDX4 and the C-terminal myc tag were detected at the cell surface by immunocytochemistry and FACS of non-permeabilised human embryonic kidney HEK 293T cells transfected with the DDX4 construct. DDX4 mRNA expression was detected in the DDX4-positive sorted cells by RT-PCR. This study clearly demonstrates that the C-terminus of DDX4 can be expressed on the cell surface despite its lack of a conventional membrane-targeting or secretory sequence. These results validate the use of antibody-based FACS to isolate DDX4-positive putative OSCs.

scholarly journals RiceFOX: A Database of Arabidopsis Mutant Lines Overexpressing Rice Full-Length cDNA that Contains a Wide Range of Trait Information to Facilitate Analysis of Gene Function

2010 ◽  
Vol 52 (2) ◽  
pp. 265-273 ◽  
Author(s):  
Tetsuya Sakurai ◽  
Youichi Kondou ◽  
Kenji Akiyama ◽  
Atsushi Kurotani ◽  
Mieko Higuchi ◽  
...  
Keyword(s):  
Gene Function ◽  
Full Length ◽  
Full Length Cdna ◽  
Wide Range ◽  
Arabidopsis Mutant ◽  
Mutant Lines

The regulation of assimilate allocation and transport

2000 ◽  
Vol 27 (6) ◽  
pp. 583 ◽  
Author(s):  
Hanjo Hellmann ◽  
Laurence Barker ◽  
Dietmar Funck ◽  
Wolf B. Frommer
Keyword(s):  
Higher Plants ◽  
Sugar Transport ◽  
Long Distance ◽  
Regulatory Pathways ◽  
Sugar Transporters ◽  
E Coli ◽  
Long Distance Transport ◽  
N Metabolism ◽  
C And N ◽  
And Storage

In higher plants, sugars possess multiplefunctions: transport and storage of carbon and energy as well as signalmolecules. A variety of sugar transporters have been cloned that showdifferential expression between source and sink tissues. Expression of thesetransporters is highly regulated, according to the local metabolic status andthe demands of long distance transport. Very little knowledge is available onmechanisms underlying the regulation of sugar transporter expression inplants. Studies in E. coli, yeast and mammals haveunravelled complex regulatory pathways with crosstalk between sugar transportand metabolism. Recent studies in plants provide increasing evidence for theexistence of similar regulatory mechanisms. In many cases, connections havebeen found between C-and N-metabolism, implicating a tight network of signaltransduction and metabolism. Some aspects of this network are presented inthis review, emphasising sugar transport and sugar signaltransduction.

scholarly journals Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 329 ◽  
Author(s):  
Anja Schmidt
Keyword(s):  
Transcriptional Activation ◽  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Higher Plants ◽  
Rna Helicases ◽  
Seed Formation ◽  
Molecular Control ◽  
Sexual And Asexual Reproduction

In higher plants, sexual and asexual reproduction through seeds (apomixis) have evolved as alternative strategies. As apomixis leads to the formation of clonal offspring, its great potential for agricultural applications has long been recognized. However, the genetic basis and the molecular control underlying apomixis and its evolutionary origin are to date not fully understood. Both in sexual and apomictic plants, reproduction is tightly controlled by versatile mechanisms regulating gene expression, translation, and protein abundance and activity. Increasing evidence suggests that interrelated pathways including epigenetic regulation, cell-cycle control, hormonal pathways, and signal transduction processes are relevant for apomixis. Additional molecular mechanisms are being identified that involve the activity of DNA- and RNA-binding proteins, such as RNA helicases which are increasingly recognized as important regulators of reproduction. Together with other factors including non-coding RNAs, their association with ribosomes is likely to be relevant for the formation and specification of the apomictic reproductive lineage. Subsequent seed formation appears to involve an interplay of transcriptional activation and repression of developmental programs by epigenetic regulatory mechanisms. In this review, insights into the genetic basis and molecular control of apomixis are presented, also taking into account potential relations to environmental stress, and considering aspects of evolution.

scholarly journals Plant Functional Genomics in A Few Days: Laser-Assisted Delivery of Double-Stranded RNA to Higher Plants

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 93
Author(s):  
Nabil Killiny ◽  
Pedro Gonzalez-Blanco ◽  
Siddarame Gowda ◽  
Xavier Martini ◽  
Ed Etxeberria
Keyword(s):  
Transgenic Plants ◽  
Gene Function ◽  
Citrus Tristeza Virus ◽  
Higher Plants ◽  
Double Stranded Rna ◽  
Assisted Delivery ◽  
Endogenous Genes ◽  
Citrus Leaves ◽  
Tristeza Virus ◽  
Citrus Trees

The technology of transgenic plants is challenging and time consuming, especially for higher plants and trees such as citrus. Double-stranded RNA (dsRNA) delivery via a plant virus is an alternative method to create transgenic plants by suppressing the expression of plant endogenous genes. Citrus tristeza virus-based vector has been constructed specifically for use in citrus trees. However, this is time-consuming, as it can take up to nine months to produce the desired phenotype. Here we describe a much faster method for the study of gene function in citrus trees. In the current study, we used laser light for the delivery of dsRNA to citrus leaves. We targeted the endogenous reporter gene phytoene desaturase (PDS) and obtained the classical phenotype (leaf bleaching) in only three days after the laser-assisted delivery. Interestingly, the phenotype response was systemic, which indicates the movement of dsRNA and/or ssRNA within the plants. In addition, dsRNAs were taken up by phloem cells and the bleaching phenotype was clear around the main veins. In conclusion, the delivery of dsRNA to plants through laser treatment may provide a fast and more specific tool to study the gene function in higher plants and trees.

scholarly journals RNA chaperones buffer deleterious mutations in E. coli

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Marina Rudan ◽  
Dominique Schneider ◽  
Tobias Warnecke ◽  
Anita Krisko
Keyword(s):  
Cold Shock Protein ◽  
Deleterious Mutations ◽  
Rna Helicases ◽  
E Coli ◽  
Dead Box ◽  
Mutator Strains ◽  
Short And Long Term ◽  
And Function ◽  
Rna Chaperones

Both proteins and RNAs can misfold into non-functional conformations. Protein chaperones promote native folding of nascent polypeptides and refolding of misfolded species, thereby buffering mutations that compromise protein structure and function. Here, we show that RNA chaperones can also act as mutation buffers that enhance organismal fitness. Using competition assays, we demonstrate that overexpression of select RNA chaperones, including three DEAD box RNA helicases (DBRHs) (CsdA, SrmB, RhlB) and the cold shock protein CspA, improves fitness of two independently evolved Escherichia coli mutator strains that have accumulated deleterious mutations during short- and long-term laboratory evolution. We identify strain-specific mutations that are deleterious and subject to buffering when introduced individually into the ancestral genotype. For DBRHs, we show that buffering requires helicase activity, implicating RNA structural remodelling in the buffering process. Our results suggest that RNA chaperones might play a fundamental role in RNA evolution and evolvability.

scholarly journals Transcriptome Analysis of the Arabidopsis Megaspore Mother Cell Uncovers the Importance of RNA Helicases for Plant Germline Development

PLoS Biology ◽  
2011 ◽  
Vol 9 (9) ◽  
pp. e1001155 ◽  
Author(s):  
Anja Schmidt ◽  
Samuel E. Wuest ◽  
Kitty Vijverberg ◽  
Célia Baroux ◽  
Daniela Kleen ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Mother Cell ◽  
Megaspore Mother Cell ◽  
Rna Helicases ◽  
Germline Development ◽  
Plant Germline

scholarly journals Modes of Reproduction and the Accumulation of Deleterious Mutations With Multiplicative Fitness Effects

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 1093-1104
Author(s):  
Patsy Haccou ◽  
Maria Victoria Schneider
Keyword(s):  
Reproductive Mode ◽  
Deleterious Mutations ◽  
Paternal Genome ◽  
Evolutionary Transitions ◽  
Synergistic Interactions ◽  
Fitness Effects ◽  
Maintenance Of Sex ◽  
Reproductive Modes ◽  
Large Populations ◽  
Lower Load

Abstract Mutational load depends not only on the number and nature of mutations but also on the reproductive mode. Traditionally, only a few specific reproductive modes are considered in the search of explanations for the maintenance of sex. There are, however, many alternatives. Including these may give radically different conclusions. The theory on deterministic deleterious mutations states that in large populations segregation and recombination may lead to a lower load of deleterious mutations, provided that there are synergistic interactions. Empirical research suggests that effects of deleterious mutations are often multiplicative. Such situations have largely been ignored in the literature, since recombination and segregation have no effect on mutation load in the absence of epistasis. However, this is true only when clonal reproduction and sexual reproduction with equal male and female ploidy are considered. We consider several alternative reproductive modes that are all known to occur in insects: arrhenotoky, paternal genome elimination, apomictic thelytoky, and automictic thelytoky with different cytological mechanisms to restore diploidy. We give a method that is based on probability-generating functions, which provides analytical and numerical results on the distributions of deleterious mutations. Using this, we show that segregation and recombination do make a difference. Furthermore, we prove that a modified form of Haldane’s principle holds more generally for thelytokous reproduction. We discuss the implications of our results for evolutionary transitions between different reproductive modes in insects. Since the strength of Muller’s ratchet is reduced considerably for several forms of automictic thelytoky, many of our results are expected to be also valid for initially small populations.

scholarly journals Differential gene expression indicates involvement of F-box proteins and E3 ligases in sexual versus apomictic germline specification in Boechera

2018 ◽  
Author(s):  
Luise Zuehl ◽  
David Ibberson ◽  
Anja Schmidt
Keyword(s):  
Gene Expression ◽  
Reproductive Mode ◽  
Differentially Expressed ◽  
Transcriptional Analysis ◽  
Tissue Type ◽  
Rna Seq ◽  
Germline Development ◽  
Ploidy Levels ◽  
E3 Ligases ◽  
Gene Regulatory

ABSTRACTGermline specification is the first step during sexual and apomictic plant reproduction. This takes place in a specialized domain of the reproductive flower tissues, the nucellus of the ovule. In each case, a sporophytic cell is determined to initiate germline development. These cells, the megaspore mother cell (MMC) or apomictic initial cell (AIC) in sexual plants and apomicts, respectively, differ in their developmental fate. While the MMC undergoes meiosis, the AIC aborts or omits meiosis to form the female gametophyte. Although these distinct developmental processes have long been described, little is known about the gene regulatory basis involved.To elucidate gene regulatory networks underlying sexual and apomictic germline specification, we conducted tissue-specific transcriptional profiling using laser-assisted microdissection and RNA-Seq. We compared the transcriptomes of the nucellar tissues harbouring the MMC or AIC between different accessions of Boechera. The six accessions we used represented four species and two ploidy levels, allowing us to distinguish between differences in gene expression caused by the genetic background or the reproductive mode.Comparative data analysis revealed widely overlapping gene expression patterns in apomictic versus sexual Boechera accessions. Nevertheless, 45 significantly differentially expressed genes were identified, which potentially play a role for determination of sexual versus apomictic reproductive mode. Interestingly, based on annotations, these include F-box proteins and E3 ligases that might relate to genes previously described as regulators important for sexual or apomictic reproduction. Thus, our findings provide new insight into the transcriptional basis of sexual and apomictic germline specification.One sentence summaryA comprehensive tissue type-specific transcriptional analysis using laser-assisted microdissection combined with RNA-Seq identifies 45 genes consistently differentially expressed during germline specification in different sexual versus apomictic Boechera accessions, indicating roles of protein degradation related to cell cycle, transcriptional and post-transcriptional regulatory processes, and stress response for apomixis.

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